Study of the origin of superstructure patterns in the scanning tunneling images of perylene-3,4,9,10-tetracarboxylic-dianhydride on graphite by electronic structure calculations

Partial electron density plots were calculated for various arrangements of perylene-3,4,9,10-tetracarboxylic-dianhydride (PTCDA) molecules on graphite to understand why scanning tunneling microscopy (STM) images of PTCDA on graphite exhibit superstructure contrast variations. In agreement with experiment, the contrast of the partial electron density plot depends strongly on the orientation and position of PTCDA on graphite. This observation originates from the fact that the overlap between the orbitals of the adsorbate and substrate is strongly affected by their relative arrangement. The HOMO or LUMO density of an adsorbate molecule can be inadequate in interpreting STM images of adsorbate molecules.